DYNAMIC CONTRIBUTIONS TO THE DNA-BINDING ENTROPY OF THE ECORI AND ECORV RESTRICTION ENDONUCLEASES

Molecular Dynamics simulations on DNA-EcoRI and DNA-EcoRV complexes su ggest that the DNA within these complexes is significantly more ordere d than free DNA. Similarly, both the protein and the DNA are more orde red in the specific (cognate) DNA-EcoRV complex than they are in the n on-cognate DNA-protein complex, consistent with recently proposed anal ogies between protein folding and sequence-specific DNA-protein recogn ition. Analysis of the trajectories shows that the net entropy gain up on specific binding to be the result of opposing contributions. Solven t release, which increases entropy versus configurational terms (as me asured by the magnitude of the atomic fluctuations), and collective te rms from tight coupling between the motions of the protein and the DNA . (C) 1996 Academic Press Limited